R Notebook

library(Seurat)
library(monocle)
library(dplyr)
library(ggplot2)

Genes to plot

Load data

#get expression values for every cell ID from the new cds
genes_df <- as.matrix(t(seurobj@data[genes, df_pdata$original_cell_id]))

Error in intI(i, n = d[1], dn[[1]], give.dn = FALSE) : 
  invalid character indexing

Pseudotime plots.

plot_grid(plotlist=plots, ncol=4)

Error in grid.newpage() : 
  could not open file '/home/cbmr/pytrik/.rstudio/notebooks/D65E8D76-10x-180831-pseudotime/1/AF50CEB7fdafc1e6/c0n9zbdwzhdwc_t/_rs_chunk_plot_001.png'

Pseudotime plots T5 precursors

genes <- c('CFD','FABP4','SAA1', 'APOE','MGP','GSN','GPX3','ADH1B','APOD','MT1X')
genes2 <- c('KRT18', 'THBS1', 'PTX3', 'CTGF', 'SERPINE2', 'TAGLN', 'TM4SF1')
df_pdata_T5 <- T5_precursors@meta.data[c('State.labels', 'Pseudotime_stretched')]
genes_df_T5 <- as.matrix(t(T5_precursors@data[unique(c(genes, genes2)),]))
df_T5 <- cbind(df_pdata_T5, as.data.frame(genes_df_T5))
plot_pseudotime_T5 <- function(gene){
  p <- ggplot(df_T5, aes_string(x='Pseudotime_stretched', y=gene)) +
    geom_point(shape = 21, colour = "black", size = 1, stroke = 0, alpha=0.2, aes(fill=State.labels), show.legend=F) +
    geom_smooth(se = FALSE, aes(color=State.labels), span=0.9, method='loess', size=2, show.legend=F)  + 
    scale_color_manual(values=c('#ede5b6')) +
    scale_fill_manual(values=colors.pseudotime.points) +
    scale_y_continuous(minor_breaks=1) +
    xlab('Pseudotime (stretched)') +
    ggtitle(gene) +
    ylab('Expression') +
    theme(plot.title = element_text(size=30), legend.text=element_text(size=30), axis.text=element_text(size=15), axis.title=element_text(size=20), legend.title=element_text(size=30), legend.key.size=unit(1.5, 'cm'))
  return(p)
}

plots <- lapply(genes, plot_pseudotime_T5)
plot_grid(plotlist=plots, ncol=3)

FeaturePlots